Sébastien Gagneux, Associate Professor, PhD

Ausserordentliche und assozierte Professorinnen/Professoren (SHIS 512)

Associate Professor of Infection Biology

Sébastien Gagneux is Associate Professor of Infection Biology and Head of the Department of Medical Parasitology and Infection Biology at the Swiss Tropical and Public Health Institute (Swiss TPH)/University of Basel. After receiving his PhD from the University of Basel, he worked as a postdoctoral fellow at Stanford University and at the Institute for Systems Biology in Seattle, USA. He then spent three years as a Program Leader at the MRC National Institute for Medical Research in London, UK before joining Swiss TPH. His research focuses on the ecology and evolution of Mycobacterium tuberculosis, and combines population genomics, molecular epidemiology and experimental approaches to study the effect of bacterial variation on host-pathogen interaction and drug resistance.

Research activities at Swiss TPH

  • Population genomics of Mycobacterium tuberculosis
  • Ecology and evolution of antibiotic resistance in Mycobacterium tuberculosis
  • Genomic epidemiology of tuberculosis

Higher education

  • MSc, 1997: Biology & Medical Parasitology, Swiss Tropical Institute/University of Basel, Switzerland
  • PhD, 2001: Epidemiology, Swiss Tropical Institute/University of Basel, Switzerland
  • 2001-2005: Postdoc, Division of Infectious Diseases & Geographic Medicine, Stanford University, USA
  • 2005-2006: Postdoc, Institute for Systems Biology, Seattle, USA

Work experience

  • 2016- : Associate Professor of Infection Biology, Swiss TPH/University of Basel, Basel, Switzerland
  • 2016- : Head of Department, Department of Medical Parasitology & Infection Biology, Swiss TPH, Basel, Switzerland
  • 2014-2016: Deputy Head of Department, Department of Medical Parasitology & Infection Biology, Swiss TPH, Basel, Switzerland
  • 2010-2016: SNF-Professor, Swiss TPH/University of Basel, Basel, Switzerland
  • 2007-2010: Programme Leader, Medical Research Council, National Institute for Medical Research, London, UK
  • 2006-2007: Senior Scientist, Institute for Systems Biology, Seattle, USA

Asare P et al. Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of household recent TB transmission in Ghana. Int J Infect Dis. 2021(in press). DOI: 10.1016/j.ijid.2021.02.110

Coscolla M et al. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb Genom. 2021(in press). DOI: 10.1099/mgen.0.000477

Guimarães A.E.D.S et al. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. Mem Inst Oswaldo Cruz. 2021;115:e200520. DOI: 10.1590/0074-02760200520

Hiza H et al. Case-control, diagnostic accuracy study of a non-sputum CD38-based TAM-TB test from a single milliliter of blood. BMJ. 2021(in press). DOI: 10.1101/2021.03.10.21253246

Ley S.D et al. Melting the eis: non-detection of kanamycin resistance markers by routine diagnostic tests and identification of new eis-promoter variants. Antimicrob Agents Chemother. 2021(in press). DOI: 10.1128/AAC.02502-20

Menardo F, Gagneux S, Freund F. Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Mol Biol Evol. 2021;38(1):290-306. DOI: 10.1093/molbev/msaa179

Menardo F et al. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res. 2021;10:60. DOI: 10.12688/f1000research.28318.1

Minja L.T et al. High burden of tuberculosis infection and disease among people receiving medication-assisted treatment for substance use disorder in Tanzania. PLoS One. 2021;16(4):e0250038. DOI: 10.1371/journal.pone.0250038

Asare P et al. Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana. Front Med (Lausanne). 2020;7:161. DOI: 10.3389/fmed.2020.00161

Castro R.A.D, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev. 2020(in press). DOI: 10.1093/femsre/fuaa071